[HTML][HTML] Structure-based virtual screening: from classical to artificial intelligence

EHB Maia, LC Assis, TA De Oliveira… - Frontiers in …, 2020 - frontiersin.org
The drug development process is a major challenge in the pharmaceutical industry since it
takes a substantial amount of time and money to move through all the phases of developing …

Forging the basis for developing protein–ligand interaction scoring functions

Z Liu, M Su, L Han, J Liu, Q Yang, Y Li… - Accounts of chemical …, 2017 - ACS Publications
Conspectus In structure-based drug design, scoring functions are widely used for fast
evaluation of protein–ligand interactions. They are often applied in combination with …

Evaluation of AutoDock and AutoDock Vina on the CASF-2013 benchmark

T Gaillard - Journal of chemical information and modeling, 2018 - ACS Publications
Computer-aided protein–ligand binding predictions are a valuable help in drug discovery.
Protein–ligand docking programs generally consist of two main components: a scoring …

Accelerating AutoDock4 with GPUs and Gradient-Based Local Search

D Santos-Martins, L Solis-Vasquez… - Journal of chemical …, 2021 - ACS Publications
AutoDock4 is a widely used program for docking small molecules to macromolecular targets.
It describes ligand–receptor interactions using a physics-inspired scoring function that has …

Application of molecular docking for the degradation of organic pollutants in the environmental remediation: A review

Z Liu, Y Liu, G Zeng, B Shao, M Chen, Z Li, Y Jiang… - Chemosphere, 2018 - Elsevier
The molecular docking has been employed successfully to study the mechanism of
biodegradation in the environmental remediation in the past few years, although medical …

Force field optimization guided by small molecule crystal lattice data enables consistent sub-angstrom protein–ligand docking

H Park, G Zhou, M Baek, D Baker… - Journal of chemical …, 2021 - ACS Publications
Accurate and rapid calculation of protein-small molecule interaction free energies is critical
for computational drug discovery. Because of the large chemical space spanned by drug …

In silico molecular docking in DNA aptamer development

TN Navien, R Thevendran, HY Hamdani, TH Tang… - Biochimie, 2021 - Elsevier
Aptamers are single-stranded DNA or RNA oligonucleotides generated by SELEX that
exhibit binding affinity and specificity against a wide variety of target molecules. Compared …

Piperine, an alkaloid of black pepper seeds can effectively inhibit the antiviral enzymes of Dengue and Ebola viruses, an in silico molecular docking study

A Nag, RR Chowdhury - Virusdisease, 2020 - Springer
Ebola and Dengue are the critical diseases caused by RNA viruses, especially in the
tropical parts of the globe, including Asia and Africa, and no prominent therapeutic options …

Molecular simulation for food protein–ligand interactions: A comprehensive review on principles, current applications, and emerging trends

Z Jin, Z Wei - Comprehensive Reviews in Food Science and …, 2024 - Wiley Online Library
In recent years, investigations on molecular interaction mechanisms between food proteins
and ligands have attracted much interest. The interaction mechanisms can supply much …

Ethylenediamine-β-cyclodextrin modified graphene oxide nanocomposite membranes for highly efficient chiral separation of tryptophan and propranolol enantiomers

X Bai, J Ke, X Qiu, H Liu, Y Ji, J Chen - Separation and Purification …, 2022 - Elsevier
The separation of racemic drugs remains significance and challenge for pharmaceutical
production. Recently, chiral drugs permeation separation based on membrane is a …